Contacts of the helix formed by residues 106 - 116 (chain A) in PDB entry 4E96
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PRO* 4.6 3.3 - - - +
83A PHE* 3.8 6.3 - - - +
85A GLN* 3.2 28.7 - - - +
86A PRO* 3.3 28.1 - - + +
87A VAL* 5.3 1.8 - - + +
105A MET* 1.3 81.7 - - - +
107A MET* 1.3 59.3 + - - +
108A GLY* 3.1 9.0 + - - -
109A THR* 2.6 39.9 + - - -
110A ILE* 3.1 28.8 + - - +
132A MET* 3.8 13.5 - - - -
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Residues in contact with MET 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.9 18.7 - - + +
74A LEU* 3.6 37.2 - - + +
75A TRP* 3.7 15.7 - - + +
80A ALA* 3.8 37.9 - - + +
83A PHE* 2.7 24.1 + - + +
84A GLN* 4.6 0.4 - - + -
106A ASP* 1.3 70.7 - - - +
108A GLY* 1.3 55.5 + - - +
110A ILE* 3.7 6.5 - - + +
111A LYS* 2.7 36.6 + - - +
129A PHE* 4.0 17.9 - - + -
132A MET* 3.7 22.9 - - + -
153A LEU* 4.8 4.5 - - + -
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Residues in contact with GLY 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TRP* 3.6 10.7 - - - -
84A GLN 3.2 26.0 + - - -
106A ASP* 3.1 6.7 + - - -
107A MET* 1.3 76.2 - - - +
109A THR* 1.4 61.6 + - - +
111A LYS* 3.7 2.6 - - - +
112A LYS* 3.2 28.2 + - - +
203A DMS 3.8 13.0 - - - -
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.8 26.4 + - + +
50A THR* 3.6 17.7 - - + +
86A PRO* 4.1 0.9 - - - +
105A MET* 3.6 17.9 - - - -
106A ASP* 2.6 35.7 + - - -
107A MET 3.2 0.2 - - - -
108A GLY* 1.4 73.0 - - - +
110A ILE* 1.3 59.0 + - - +
112A LYS 3.5 0.5 + - - -
113A ARG* 3.0 57.5 + - - +
203A DMS 4.0 12.6 - - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 4.7 2.0 - - + -
105A MET* 4.0 6.1 - - + -
106A ASP 3.1 20.8 + - - +
107A MET* 3.7 9.4 - - + +
109A THR* 1.3 72.2 - - - +
111A LYS* 1.3 62.6 + - - +
113A ARG* 3.4 2.1 + - - +
114A LEU* 2.9 42.5 + - + +
119A TYR* 3.8 15.9 + - - +
125A CYS* 4.0 2.7 - - - -
128A ASP* 3.8 22.0 - - + +
129A PHE* 3.7 67.5 - - + +
132A MET* 5.0 2.5 - - - -
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.4 4.6 - - + +
71A LEU* 3.9 28.9 - - + -
75A TRP* 3.8 42.4 - - + +
107A MET 2.7 21.8 + - - +
108A GLY* 3.7 4.9 - - - +
110A ILE* 1.3 75.1 - - - +
112A LYS* 1.3 59.7 + - + +
114A LEU* 3.2 6.3 + - - +
115A GLU* 2.5 67.1 + - + +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 3.5 26.0 - - + +
108A GLY 3.2 14.1 + - - +
111A LYS* 1.3 80.5 - - + +
113A ARG* 1.3 52.2 + - - +
115A GLU* 3.1 19.0 + - - +
116A ASN* 2.6 47.9 + - - +
203A DMS 3.0 33.5 - - + +
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.8 16.4 - - - +
49A GLU* 2.8 29.4 + - - +
50A THR* 3.9 17.2 - - - +
105A MET* 3.7 12.6 - - - +
109A THR* 3.0 30.0 + - - +
110A ILE* 3.5 4.5 - - - +
112A LYS* 1.3 75.1 - - - +
114A LEU* 1.3 59.7 + - - +
117A ASN 3.1 3.1 + - - -
118A TYR* 2.8 73.9 + - + +
119A TYR* 3.5 26.0 - - + +
128A ASP* 2.7 36.5 + - - -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.8 35.2 - - + +
66A LEU* 3.9 10.8 - - + +
67A LEU* 3.8 44.0 - - + +
71A LEU* 4.3 7.2 - - + -
110A ILE* 2.9 38.0 + - + +
111A LYS 3.6 3.4 - - - +
113A ARG* 1.3 73.2 - - - +
115A GLU* 1.3 62.6 + - - +
117A ASN* 3.2 20.7 + - - +
119A TYR* 3.7 25.8 - - + -
125A CYS* 4.0 9.9 - - - -
129A PHE* 5.2 0.7 - - + -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.3 21.0 - - + +
111A LYS* 2.5 56.6 + - - +
112A LYS* 3.4 22.0 + - - +
114A LEU* 1.3 76.6 - - - +
116A ASN* 1.3 63.9 + - - +
117A ASN* 3.4 7.3 + - - +
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Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 3.3 38.2 + - - +
51A SER* 3.9 12.9 + - - +
57A LYS* 4.8 3.1 - - - +
112A LYS* 2.6 26.6 + - - +
113A ARG 3.3 2.6 + - - +
114A LEU 3.2 0.2 - - - -
115A GLU* 1.3 80.7 - - - +
117A ASN* 1.3 71.6 - - - +
118A TYR* 3.2 3.3 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il